Project Summary Multiple lines of evidence suggest that balancing selection is pervasive across a wide range of organisms. However, debate remains regarding how much of the genome is influenced by balancing selection, and over what time scales functional genetic diversity is maintained. In sexual systems, balancing selection can maintain genetic diversity over only small portions of the genome. In contrast, asexual organisms experience complete linkage and balancing selection can maintain diversity genome-wide. Many organisms utilize a mix of both sexual and asexual reproduction. Organisms with mixed reproductive strategies exhibit unique evolutionary dynamics. Notably, elevated linkage may be maintained over long distances, potentially facilitating the evolution of linked, co-adapted gene complexes, similar to inversions or areas of low recombination. We propose that in cyclic parthenogens, the presence of linked, coadapted gene complexes may result in large blocks of the genome being subject to balancing selection. The overarching goal of this proposal is to test for the presence and mode of balancing selection in cyclic parthenogens and assess its impact on the patterns of genetic diversity genome-wide. I propose to study a natural metapopulation of the model cyclic parthenogen, Daphnia pulex to perform this work, and will utilize computational, field-based, and genomic approaches. Daphnia are ideal for addressing the genomic consequences of balancing selection as they have been demonstrated to respond rapidly to selection across a single growing season suggesting abundant, fitness related genetic variation. Distinct clonal lineages nonetheless persist over time in the field and lab suggesting a stabilizing force, such as balancing selection. Daphnia are easily sampled in large numbers across space and time, are amenable to laboratory manipulation, have a growing collection of genomic and genetic resources, and are an ecological/ecotoxological model system providing a rich context in which to place our proposed work. To determine the prevalence of balancing selection and its impact on patterns of genetic diversity I will first use genome wide sequence data and RNAseq to test the prediction of functional differentiation between co-existing clonal lineages of D. pulex. Second, I will use seasonal sampling and sequencing to test for evidence of two potential mechanisms of balancing selection in populations of D. pulex. Finally, I will use sequence data to determine the proportion of the genome impacted by balancing selection, and the ability of balancing selection to maintain functionally divergent blocks of the genome across space and time. This work will inform our understanding of the functional significance of standing genetic diversity in natural populations, with implications for understanding the evolution of humans and their pathogens, in particular expanding our understanding to include pathogens with mixed reproductive systems (e.g. trematodes).